When we reach Fleet Admiral it's only right that we command a small fleet, right? But how to implement such a system while still maintaining the game's core game-play mechanics? The answer is simple: Support Ships.

Support ships would basically operate the way BOs do on the ground, only in space; but that is an oversimplification of a more complex proposal, so without further adieu:

1) Basic Class Breakdown and Specialization

Now as with BOs there are three basic types of Support Ships:

Science Vessels - Science
Cruisers - Engineering
Escorts - Tactical

With an extra fourth class for filling out incomplete groups:

Light Cruisers - Red Shirts

Now as with BOs the individual Ship classes are specialized for their respective fields, namely able to use the high level versions of the appropriate space powers (Escorts can use HYT III while Cruisers and Science Ships can't etc.), but seeing as they are starships and not single individuals a Support Ship can have powers from all three branches.
2) Powers and Skill Points

As was mentioned above your Support Ships have access to Space BO powers and will be specialized for using powers from their specific branch over those of the other branches:

For the sake of manageability, I would suggest giving the Support Ships a maximum of four powers.

Like with BOs, these powers will need to be leveled up for maximum performance. In order to level up your Support Ship's powers you will need to invest BO Skill Points, as this is a starship we are talking about, however, the point cost would be higher (Exactly how much higher is open for debate).

3) The Refit System

What is the Refit System you ask? The refit system is like when you rank up your BOs , only for your Support Ships. All Support ships (With the exception of the Light Cruisers) start out as Tier 2 ships (Constitution, Saber, and Nova class plus variants). Once you have invested enough Skill Points in a Support Ship (Ideally enough to have maxed out the first skill) you will be able to refit your Support Ship and effectively increase its Tier. With this increase the Support Ship gains the appropriate amount of weapons and hull , access to the Support Ship's next ability, and the option of changing the ship itself to the next tier (Saber class to Akira class for example) though this would be merely cosmetic and would not affect the hull and weapons upgrade.
4) Rarity and Assigning and Customizing the Captain

As with BOs Support ships come in varying degrees of rarity from common whites to very rare purples. Unlike BO's however a Support Ship's rarity can be changed; after all everyone knows it is the captain and crew that make a ship special. When you receive a support Ship you get the option to assign it a new captain at any time by selecting one of your bridge officers (assigned or not) and giving them command of the Support Ship, which will then take on the rarity of the assigned captain. Of course you can't just assign any officer to any ship, unlike player ships each Support Ship can take only one type of BO as a captain:

Be Warned, however, as this assignment is PERMANENT and you will not be able to get any BOs back once they have been made captain.

Should you decide not to assign a new captain right away or you make an unassigned BO the Support Ship's captain, you will have the option to customize said captain's appearance for free. The Support Ship's default captain offers full customization (species, gender, the works) while making an unassigned BO captain will limit you to that BO's species and gender. Needless to say, should you make an assigned BO captain of a Support Ship you will not get the option of free customization.

5) Support Ship Management

Of course all this raises a couple of questions: Can I control my Support Ships? What happens when a Support Ship is killed?
Now Ideally you would have the same level of control over the actions of your Support Ships as you do over your BOs (What they target, whether or not they attack, what powers they use) with the possible exception of way-points.
As for Support Ships getting killed, the easiest solution is to have Support Ships be disabled and and the player, or another Support Ship, be able to fly near them and beam over a repair team to "revive" the ship much like with BOs on the ground.

6) Effects on the Experience and Making it Optional

Needless to say entering a battle with Support Ships would be a different experience from entering it without them and as such some adjustments would have to be made, and at the same time this sort of game-play might not be everyone's cup of tea. So how do we reconcile these factors? Make it optional. While players would still be given Support Ships as they level up they would be given a choice before entering a mission to play in "Normal Mode" or in "Fleet Admiral Mode" (Names subject to change). Normal mode would put you into the action much as it is now: just you, your ship, and some enemies or whatever the mission dictates. Fleet Admiral mode, however would pit you up against more enemies, harder enemies, or a combination of the two. For instance, in Normal mode, you may fight a Borg Cube at the end of a mission, while in Fleet Admiral mode you may fight two Cubes or even a Tactical Cube.

Conclusion

Well, there you have it folks, a way to make game-play at Fleet Admiral different and engaging while not changing too much of the way the game is played. Thank you for reading and feel free to leave any feedback or suggestions.